PandemicModel

Repository for Delineo Disease Modeling at the Johns Hopkins University.

Developer Notes

Choose one of the below, either a local dev environment or a Conda environment.

Setting up local dev environment

1. Ensure you have python3.8 installed and set up.
2. Clone this repository.
3. Initialize a virtual environment: python3.8 -m venv ~/.envs/PandemicModel. (Consider using virtualenvwrapper for steps 3-4)
4. Activate the virtual environment: source ~/.envs/PandemicModel/bin/activate.
5. Install dependencies: pip install -r requirements.txt.

Setting up Conda environment

1. In the Anaconda CMD.exe Prompt, create a new environment with conda create -n myenv python=3.9.1, where myenv is the name of the environment. Python version 3.9.1 is what's up and running on the covidmod server so it's a good choice to use for your conda environment.
2. Activate the conda environment with conda activate myenv.
3. Clone this repository.
4. Navigate into the PandemicModel folder and run pip install -r requirements.txt.

For both, the best way to verify everything is working is to navigate into the simulation folder and try running python master.py. If you get a bunch of numbers spit out to your terminal, then you're all set.

Troubleshooting

• Most likely, you will run into issues due to some dependency not being installed in your conda environment/virtual env. Check ClickUp and/or Slack for a full list of working dependencies.
• If you get an error along the lines of synthpops has no attribute 'validate' in population.py, open up an editor and uncomment the first synthpops import, and comment the second one out.

Misc.

• Please do not commit venv stuff.
• If you pip install anything, remember to pip freeze > requirements.txt before committing any changes.
• You cannot commit to the master branch, remember to commit all changes to a new branch and open a PR when you're ready to merge.

Important Folders/Files

All important files for running are in the /simulation folder

simulation/diseasedata: contains comorbidity data
simulation/synthpops: DO NOT TOUCH unless you really know what you're doing
simulation/master.py: runs the simulation- call this file on command line to get a result